Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning

The production of commercial DNA microarrays is based on a light-directed chemical synthesis driven by a set of masks or micromirror arrays. Because of the natural properties of light and the ever shrinking feature sizes, the arrangement of the probes on the chip and the order in which their nucleotides are synthesized play an important role on the quality of the final product. We propose a new model called conflict index for evaluating the layout of microarrays. We also present a new algorithm, called Pivot Partitioning, that improves the quality of layouts, according to existing measures, by over 6% when compared to the best known algorithms.